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Mehrabi Sisakht J, Mehri M, Najmabadi H, Azarkeivan A, Neishabury M. Genetic Diagnosis of Pyruvate Kinase Deficiency in Undiagnosed Iranian Patients with Severe Hemolytic Anemia, using Whole Exome Sequencing. ARCHIVES OF IRANIAN MEDICINE 2022; 25:691-697. [PMID: 37542401 PMCID: PMC10685872 DOI: 10.34172/aim.2022.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/28/2021] [Indexed: 08/06/2023]
Abstract
BACKGROUND After ruling out the most common causes of severe hemolytic anemia by routine diagnostic tests, certain patients remain without a diagnosis. The aim of this study was to elucidate the genetic cause of the disease in these patients using next generation sequencing (NGS). METHODS Four unrelated Iranian families including six blood transfusion dependent cases and their parents were referred to us from a specialist center in Tehran. There was no previous history of anemia in the families and the parents had no abnormal hematological presentations. All probands presented severe congenital hemolytic anemia, neonatal jaundice and splenomegaly. Common causes of hemolytic anemia were ruled out prior to this investigation in these patients and they had no diagnosis. Whole exome sequencing (WES) was performed in the probands and the results were confirmed by Sanger sequencing and subsequent family studies. RESULTS We identified five variants in the PKLR gene, including a novel unpublished frameshift in these families. These variants were predicted as pathogenic according to the ACMG guidelines by Intervar and/or Varsome prediction tools. Subsequent family studies by Sanger sequencing supported the diagnosis of pyruvate kinase deficiency (PKD) in six affected individuals and the carrier status of disease in their parents. CONCLUSION These findings show that PKD is among the rare blood disorders that could remain undiagnosed or even ruled out in Iranian population without performing NGS. This could be due to pitfalls in clinical, hematological or biochemical approaches in diagnosing PKD. Furthermore, genotyping PKD patients in Iran could reveal novel mutations in the PKLR gene.
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Affiliation(s)
- Jafar Mehrabi Sisakht
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maghsood Mehri
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Azita Azarkeivan
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Maryam Neishabury
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Rehman AU, Rashid A, Hussain Z, Shah K. A novel homozygous missense variant p.D339N in the PKLR gene correlates with pyruvate kinase deficiency in a Pakistani family: a case report. J Med Case Rep 2022; 16:66. [PMID: 35168679 PMCID: PMC8848962 DOI: 10.1186/s13256-022-03292-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/18/2022] [Indexed: 01/19/2023] Open
Abstract
Background Pyruvate kinase deficiency is an exceptionally rare autosomal recessive Mendelian disorder caused by bi-allelic pathogenic variants in the PKLR gene. It is mainly characterized by chronic nonspherocytic hemolytic anemia though other symptoms such as splenomegaly, hepatomegaly, pallor, fatigue, iron overload, shortness of breath, hyperbilirubinemia, and gallstones might also prevail. Case presentation We present here a novel genetic defect in the PKLR gene that correlates with pyruvate kinase deficiency phenotype in a consanguineous family from North-Western Pakistan. The family included three affected individuals who were all born to consanguineous parents. The proband, a 13-year-old female of Pashtun ethnicity, showed chronic nonautoimmune hemolytic anemia since birth, extremely low hemoglobin (7.6 g/dL) and pyruvate kinase (12.4 U/g Hb) levels, splenomegaly, and hepatomegaly. Bone marrow aspirate showed a markedly decreased myeloid to erythroid ratio and hypercellular marrow particles due to hyperplasia of the erythroid elements. Molecular characterization of the proband’s genomic DNA uncovered a likely pathogenic homozygous missense variant p.[D339N] in exon 7 of the PKLR gene. In-depth in silico analysis and familial cosegregation implies p.[D339N] as the likely cause of pyruvate kinase deficiency in this family. Further in vitro or in vivo studies are required to validate the impact of p.[D339N] on protein structure and/or stability, and to determine its role in the disease pathophysiology. Conclusions In summary, these findings suggest a novel genetic defect in the PKLR gene as a likely cause of pyruvate kinase deficiency, thus further expanding the mutational landscape of this rare Mendelian disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s13256-022-03292-z.
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Affiliation(s)
- Atta Ur Rehman
- Department of Biomedical Sciences, Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Khanpur Road, Mang, Haripur, Pakistan.
| | - Abdur Rashid
- Department of Higher Education Archives and Libraries Peshawar, Government of Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Zubair Hussain
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Khadim Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
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Secrest MH, Storm M, Carrington C, Casso D, Gilroy K, Pladson L, Boscoe AN. Prevalence of pyruvate kinase deficiency: A systematic literature review. Eur J Haematol 2020; 105:173-184. [PMID: 32279356 PMCID: PMC7496626 DOI: 10.1111/ejh.13424] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 01/19/2023]
Abstract
OBJECTIVES Pyruvate kinase deficiency (PK deficiency) is a rare disorder caused by compound heterozygosity or homozygosity for > 300 mutations in the PKLR gene. To understand PK deficiency prevalence, we conducted a systematic literature review. METHODS We queried Embase and Medline for peer-reviewed references reporting PK deficiency prevalence/incidence, PKLR mutant allele frequency (MAF) among the general population, or crude results from which these metrics could be derived. RESULTS Of 1390 references screened, 1296 were excluded after title/abstract review; 60 were excluded after full-text review. Four of the remaining 34 studies were considered high-quality for estimating PK deficiency prevalence. Two high-quality studies identified cases from source populations of known sizes, producing estimates of diagnosed PK deficiency prevalence of 3.2 and 8.5 per million. Another high-quality study derived an estimate of diagnosed PK deficiency prevalence of 6.5 per million by screening jaundiced newborns. The final high-quality study estimated total diagnosed and undiagnosed PK deficiency prevalence to be 51 per million through extrapolation from observed MAFs. CONCLUSIONS We conclude that prevalence of clinically diagnosed PK deficiency is likely between 3.2 and 8.5 per million in Western populations, while the prevalence of diagnosed and undiagnosed PK deficiency could possibly be as high as 51 per million.
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Affiliation(s)
| | - Mike Storm
- Agios Pharmaceuticals Inc.CambridgeMAUSA
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Li H, Gu P, Yao RE, Wang J, Fu Q, Wang J. A novel and a previously described compound heterozygous PKLR gene mutations causing pyruvate kinase deficiency in a Chinese child. Fetal Pediatr Pathol 2014; 33:182-90. [PMID: 24601847 DOI: 10.3109/15513815.2014.890260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Pyruvate kinase deficiency (PKD) is one of the most common enzymatic defects in humans and it is an autosomal recessive disorder causing chronic nonspherocytic hemolytic anemia. METHODS A two-year-old male baby with severe hemolytic anemia and low level of pyruvate kinase (PK) activity was enrolled in this study. All exons of PKLR gene and their flanking sequences were amplified from the patient's genomic DNA using PCR. Bioinformatics software was used to evaluate the functional impacts of the mutations found in this study. RESULTS It was here demonstrated that the boy harbored a previously described mutation (c. 941T>C) in exon 7 and a novel mutation (c. 1183 G>C) in exon 9 of PKLR gene. Both mutations led to significant structural alterations and decreased enzymatic activity of PK, as predicted by tool software. CONCLUSIONS The compound heterozygous mutations in the PKLR gene were the cause of inherited PKD for this patient.
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Affiliation(s)
- Huimin Li
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine , Shanghai , China
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Machado P, Manco L, Gomes C, Mendes C, Fernandes N, Salomé G, Sitoe L, Chibute S, Langa J, Ribeiro L, Miranda J, Cano J, Pinto J, Amorim A, do Rosário VE, Arez AP. Pyruvate kinase deficiency in sub-Saharan Africa: identification of a highly frequent missense mutation (G829A;Glu277Lys) and association with malaria. PLoS One 2012; 7:e47071. [PMID: 23082140 PMCID: PMC3474807 DOI: 10.1371/journal.pone.0047071] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023] Open
Abstract
Background Pyruvate kinase (PK) deficiency, causing hemolytic anemia, has been associated to malaria protection and its prevalence in sub-Saharan Africa is not known so far. This work shows the results of a study undertaken to determine PK deficiency occurrence in some sub-Saharan African countries, as well as finding a prevalent PK variant underlying this deficiency. Materials and Methods Blood samples of individuals from four malaria endemic countries (Mozambique, Angola, Equatorial Guinea and Sao Tome and Principe) were analyzed in order to determine PK deficiency occurrence and detect any possible high frequent PK variant mutation. The association between this mutation and malaria was ascertained through association studies involving sample groups from individuals showing different malaria infection and outcome status. Results The percentage of individuals showing a reduced PK activity in Maputo was 4.1% and the missense mutation G829A (Glu277Lys) in the PKLR gene (only identified in three individuals worldwide to date) was identified in a high frequency. Heterozygous carrier frequency was between 6.7% and 2.6%. A significant association was not detected between either PK reduced activity or allele 829A frequency and malaria infection and outcome, although the variant was more frequent among individuals with uncomplicated malaria. Conclusions This was the first study on the occurrence of PK deficiency in several areas of Africa. A common PKLR mutation G829A (Glu277Lys) was identified. A global geographical co-distribution between malaria and high frequency of PK deficiency seems to occur suggesting that malaria may be a selective force raising the frequency of this 277Lys variant.
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Affiliation(s)
- Patrícia Machado
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Licínio Manco
- Centro de Investigação em Antropologia e Saúde (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Cláudia Gomes
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Cristina Mendes
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Natércia Fernandes
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Graça Salomé
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Luis Sitoe
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Sérgio Chibute
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - José Langa
- Banco de Sangue do Hospital Central de Maputo, Maputo, Mozambique
| | - Letícia Ribeiro
- Departmento de Hematologia, Centro Hospitalar de Coimbra, Coimbra, Portugal
| | | | - Jorge Cano
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III, Madrid, Spain
| | - João Pinto
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - António Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Virgílio E. do Rosário
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Paula Arez
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail:
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